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New Insights into Satellite DNAs

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 March 2025 | Viewed by 3197

Special Issue Editors


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Guest Editor
1. Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
2. Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
Interests: satellite DNA; heterochromatin; gene regulation; epigenetics; DNA repair
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Guest Editor
Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
Interests: satellite DNA; satellite RNA; heterochromatin; gene regulation; epigenetics

Special Issue Information

Dear Colleagues,

Located in the (peri)centromeric and subtelomeric heterochromatin, satellite DNAs contribute significantly to the genome architecture, and identical satellite DNA repeats on multiple chromosomes were shown to be important for chromocenter formation and genome maintenance. Apart from that, satellite DNAs are characterized by high sequence homogeneity between populations of the same species, and the specific sequence variability among closely related species has suggested their role in genome evolution and speciation process. Satellite DNAs are also involved in important roles in stress cell physiology and gene regulation. Moreover, changes in satellite DNA structure and transcription activity associated with the disturbance of the heterochromatin are linked with diseases such as cancer, as well as senescence and aging. Satellite RNAs were also shown to act as cancer biomarkers, and the role of satellite DNA in targeted drug therapy for cancer was recently proposed. However, new studies are necessary to explain the regulation of satellite DNA transcription and epigenetic changes associated with satellite DNA and heterochromatin during different cellular processes.

This Special Issue addresses all kinds of research related to our current knowledge on satellite DNA structure, organization and evolution, as well as the regulation of transcription, and diverse roles of satellite DNAs and their transcripts, e.g., for centromere and heterochromatin establishment, genome integrity or gene regulation. We would also like to underline the genetic or epigenetic alteration of satellite DNAs and heterochromatin during cellular processes, as well as in diseases and aging. We look forward to receiving your contributions in the form of original research or review articles.

Dr. Isidoro Feliciello
Prof. Dr. Đurđica Ugarković
Guest Editors

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Keywords

  • satellite DNA
  • satellitome
  • satellite DNA organization
  • satellite DNA evolution
  • satellite DNA origin
  • satellite DNA transcription
  • satellite DNA function
  • satellite DNA regulation
  • satellite RNA
  • heterochromatin
  • centromere
  • telomere
  • gene regulation
  • cancer
  • biomarkers
  • epigenetics
  • next-generation sequencing (NGS)
  • nanopore sequencing
  • PacBio sequencing

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Published Papers (2 papers)

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Research

13 pages, 2185 KiB  
Article
Novel Cascade Alpha Satellite HORs in Orangutan Chromosome 13 Assembly: Discovery of the 59mer HOR—The largest Unit in Primates—And the Missing Triplet 45/27/18 HOR in Human T2T-CHM13v2.0 Assembly
by Matko Glunčić, Ines Vlahović, Marija Rosandić and Vladimir Paar
Int. J. Mol. Sci. 2024, 25(14), 7596; https://doi.org/10.3390/ijms25147596 - 11 Jul 2024
Cited by 1 | Viewed by 1128
Abstract
From the recent genome assembly NHGRI_mPonAbe1-v2.0_NCBI (GCF_028885655.2) of orangutan chromosome 13, we computed the precise alpha satellite higher-order repeat (HOR) structure using the novel high-precision GRM2023 algorithm with Global Repeat Map (GRM) and Monomer Distance (MD) diagrams. This study rigorously identified alpha satellite [...] Read more.
From the recent genome assembly NHGRI_mPonAbe1-v2.0_NCBI (GCF_028885655.2) of orangutan chromosome 13, we computed the precise alpha satellite higher-order repeat (HOR) structure using the novel high-precision GRM2023 algorithm with Global Repeat Map (GRM) and Monomer Distance (MD) diagrams. This study rigorously identified alpha satellite HORs in the centromere of orangutan chromosome 13, discovering a novel 59mer HOR—the longest HOR unit identified in any primate to date. Additionally, it revealed the first intertwined sequence of three HORs, 18mer/27mer/45mer HORs, with a common aligned “backbone” across all HOR copies. The major 7mer HOR exhibits a Willard’s-type canonical copy, although some segments of the array display significant irregularities. In contrast, the 14mer HOR forms a regular Willard’s-type HOR array. Surprisingly, the GRM2023 high-precision analysis of chromosome 13 of human genome assembly T2T-CHM13v2.0 reveals the presence of only a 7mer HOR, despite both the orangutan and human genome assemblies being derived from whole genome shotgun sequences. Full article
(This article belongs to the Special Issue New Insights into Satellite DNAs)
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18 pages, 3546 KiB  
Article
Genome Variability in Artificial Allopolyploid Hybrids of Avena sativa L. and Avena macrostachya Balansa ex Coss. et Durieu Based on Marker Sequences of Satellite DNA and the ITS1–5.8S rDNA Region
by Alexandra V. Amosova, Alexander A. Gnutikov, Alexander V. Rodionov, Igor G. Loskutov, Nikolai N. Nosov, Olga Yu. Yurkevich, Tatiana E. Samatadze, Svyatoslav A. Zoshchuk and Olga V. Muravenko
Int. J. Mol. Sci. 2024, 25(10), 5534; https://doi.org/10.3390/ijms25105534 - 19 May 2024
Cited by 1 | Viewed by 1485
Abstract
Artificial hybrids between cultivated Avena species and wild Avena macrostachya that possess genes for resistance to biotic and abiotic stresses can be important for oat breeding. For the first time, a comprehensive study of genomes of artificial fertile hybrids Avena sativa × Avena [...] Read more.
Artificial hybrids between cultivated Avena species and wild Avena macrostachya that possess genes for resistance to biotic and abiotic stresses can be important for oat breeding. For the first time, a comprehensive study of genomes of artificial fertile hybrids Avena sativa × Avena macrostachya and their parental species was carried out based on the chromosome FISH mapping of satellite DNA sequences (satDNAs) and also analysis of intragenomic polymorphism in the 18S–ITS1–5.8S rDNA region, using NGS data. Chromosome distribution patterns of marker satDNAs allowed us to identify all chromosomes in the studied karyotypes, determine their subgenomic affiliation, and detect several chromosome rearrangements. Based on the obtained cytogenomic data, we revealed differences between two A. macrostachya subgenomes and demonstrated that only one of them was inherited in the studied octoploid hybrids. Ribotype analyses showed that the second major ribotype of A. macrostachya was species-specific and was not represented in rDNA pools of the octoploids, which could be related to the allopolyploid origin of this species. Our results indicate that the use of marker satDNAs in cytogenomic studies can provide important data on genomic relationships within Avena allopolyploid species and hybrids, and also expand the potential for interspecific crosses for breeding. Full article
(This article belongs to the Special Issue New Insights into Satellite DNAs)
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